if you swap key and transponder box along with the ecu it doesnt need recoding with vagcom, mat says he cant get it vag-com cable working so needs to do it this way

Also says with ecu swapped car starts then dies which is an immobilisor fault.
I beleive if you just swap ecu you can recode the matched key and transponder box to the new ecu as cs98sss4 said

edit: I saved this text from clubgti somewhere, this is how you adapt a transponder box to an ecu apparently:
To Adapt Immobiliser:
Go to 'Immobiliser' Module in VAG-Com,
'Adaptation'
Then 'Read'
Wait a few seconds, and press 'Save'.
To Adapt ECU:
Go to 'Engine' Module in VAG-Com,
'Adaptation'
Then 'Read'
Wait a few seconds, and press 'Save'.
Do both...and all works well.
I've swapped them about many times. Never a problem.
This just seems to mate the immobiliser to the engine ECU.